Abstract
Grapevine fabavirus (GFabV) was identified in the ‘Xiangfei’ grapevine in Liaoning, China, by small RNA sequencing. The complete nucleotide sequences of genomic RNA1 and RNA2 of the XF isolate were determined. The sizes of genomic RNA1 and RNA2 of XF isolate were 5 822 and 3 134 nucleotides (nt) respectively. Compared to other available GFabV genomes, XF isolate showed 81.7 ~82.7% and 84.8 ~94.9% in RNA1 polyprotein gene, and 67.2 ~82.8% and 78.0 ~96.1% in RNA2 polyprotein, at the nt and amino acid (aa) level, respectively. Phylogenetic analysis of complete and nearly complete genomic sequences of GFabV isolates showed XF form a separate evolutionary branch. This paper is the first report of the complete genome of GFabV in China.
References
Al Rwahnih M, Alabi OJ, Westrick NM, Golino D, Rowhani A (2016) Near-complete genome sequence of grapevine fabavirus, a novel putative member of the genus Fabavirus. Genome Announc 4:e00703–e00716
Chiaki Y, Ito T, Sato A, Sugiura H, Nishimura R (2020a) Dwarfing caused by viral pathogens and leaf malformations in ‘Shine Muscat’ grapevine. J Gen Plant Pathol 86:34–38
Chiaki Y, Ito T, Nakaune R (2020b) Genetic variability of grapevine fabavirus variants and development of a broad-spectrum assay for their detection. Arch Virol 165:2073–2078
Fan XD, Dong YF, Zhang ZP, Zhang MY, Ren F, Hu GJ (2019) Small RNA sequencing and RT-PCR detection of viruses infecting ‘Shine Muscat’ grapevines. Acta Phytopathologica Sinica 49:749–755
Fan XD, Zhang MY, Zhang ZP, Ren F, Hu GJ, Dong YF (2020) Prevalence and genetic diversity of grapevine fabavirus isolates from different grapevine cultivars and regions in China. J Integr Agric 19:768–774
Jo Y, Song MK, Choi H, Park JS, Lee JW, Cho WK (2017) First Report of Grapevine fabavirus in Diverse Vitis Species in Korea. Plant Dis 101:1829
Joshi CP, Zhou H, Huang X, Chiang VL (1997) Context sequence of translation initiation codon in plants. Plant Mol Biol 35:993–1001
Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Gen Res 18:821–829
Acknowledgements
This study was supported by China Agriculture Research System of MOF and MARA (CARS-29-bc-1), and National key R&D Program of China (2019YFD1001800). The authors declare that they have no competing interests.
Author information
Authors and Affiliations
Corresponding authors
Ethics declarations
Ethical approval
This article does not contain any studies with human participants or animals performed by any of the authors.
Conflict of interest
The authors declare that they have no competing interests.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Zhang, M., Zhang, B., Zhang, Z. et al. Complete nucleotide sequence of a divergent variant of grapevine fabavirus from northeastern China. J Plant Pathol 104, 3–8 (2022). https://doi.org/10.1007/s42161-021-00991-2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s42161-021-00991-2